The complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994 (Decapoda: Rhynchocinetidae)

Abstract We report the complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994. The mitogenome was found to contain 16158 bp with 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs), and 1 putative control region. Phylogenetic analysis indicated that R. brucei was sister to Rhynchocinetes durbanensis (PP= 1), of the same family Rhynchocinetidae. These results are helpful for research on the phylogenetic and evolutionary studies of this group.


Introduction
Rhynchocinetes brucei (Decapoda: Rhynchocinetidae) is widely distributed in the Philippines, Hong Kong, and the Great Barrier Reef in the tropical West Pacific (Okuno 1994).The mate guarding behavior displayed by R. brucei is rarely observed among caridean shrimp (Martin et al. 2010).The distinguishing features of this species include intricate red bands that cover the entire surface, a notable dark red spot located on the back of the third abdominal segment (Figure 1), and articular gills on its first three pairs of pereiopods (Okuno 1994).There is only one complete mitochondrial genome of the family Rhynchocinetidae in the NCBI GenBank (Rhynchocinetes durbanensis, KT590405).In this study, we first recorded this species in the East China Sea and reported the complete mitochondrial genome of R. brucei, which provided molecular information for research on the phylogenetic and evolutionary studies of this group.

Materials
The studied specimen of R. brucei used in this study was collected from rocks of Nanji Islands, East China Sea (27 � 27'28.24"N,121 � 4'39.63"E,water depth 6 m) on 18 July 2021.The specimen was fixed and preserved in 100% ethanol, and finally deposited in the Institute of Oceanology, Chinese Academy of Sciences (IOCAS) in Qingdao, China (contact: Hangjun Wang, wanghj@ecs.mnr.gov.cn)under the voucher number MBM189207.

Methods
DNA extraction, sequencing, and clean data were performed according to the methods used by Li et al. (2023).The raw data, including 34,590,902 reads amounting to 5.19 G.To check the consistency of results from different assembly strategies, two methods, i.e.GetOrganelle v1.7.6.1 (Jin et al. 2020) andNovoPlasty v. 4.3.1 (Dierckxsens et al. 2017) were used for assembly.
To evaluate the quality of assembly, clean reads were mapped to the obtained contig using a subcommand mitoz visualize of MitoZ v3.6 (Meng et al. 2019) to show the coverage depth.The coverage depth of the assembled mitochondrial genome was calculated by applying the samtools depth command in Samtools v.1.6(Danecek et al. 2021), and a coverage map was generated using Circos v.0.69 (Krzywinski et al. 2009).Annotation of the mitochondrial genome was carried out using the MITOS2 (Donath et al. 2019) and the MitoZ annotation module (Meng et al. 2019).The two results of annotation were loaded into Geneious v2021.0.3.and checked manually with the help of ORFs (finds open reading frames).The final mitogenome sequence was visualized using the visualize subcommand in MitoZ v3.6 (Meng et al. 2019).Strand asymmetry was calculated using the formulae: (Perna and Kocher 1995).
Bayesian Inference phylogenies were inferred using MrBayes v3.2.7a (Ronquist et al. 2012) under a partition model (2 parallel runs, 2000000 generations), in which the initial 25% of sampled data were discarded as burn-in.Finally, we used iTOL v6 (Letunic and Bork 2016) to visualize the derived BI tree.
The BI phylogenetic tree, based on 13 PCGs, showed that R. brucei was the sister to R. durbanensis (PP ¼ 1), and Rhynchocinetidae was closer to Hippolytidae (Figure 3).

Discussion and conclusion
In this study, we first reported the full mitochondrial genome of R. brucei and gave a detailed annotation.To ensure the reliability of the assembly, we employed two distinct assembly methods, namely GetOrganelle and NovoPlasty.We found that ATP8 gene of the R. brucei is difficult to annotate using MITOS2 and MitoZ, so we annotated it using find ORFs function in Geneious and compared it with other mitochondrial genomes in the infraorder Caridea.Other technologies such as transcriptomics sequencing may be helpful for the reliability of ATP8 annotation.

Figure 3 .
Figure 3. Phylogenetic analysis (Bayesian Inference) of R. brucei on the whole mitochondrial genome sequences.The tree was constructed based on concatenated nucleotide sequences of 13 protein-coding genes (PCGs) of 19 species in 8 families.The numbers under the internodes represent Bayesian inference (BI) posterior probabilities (PP).GenBank accession numbers used are listed after the species names.The scale bar indicates the number of substitutions per site.

Figure 2 .
Figure 2. The complete mitogenome of R. brucei.The innermost and Middle circles depict the GC content and distribution of sequencing depth, respectively.The outermost circle indicates the arrangements of genes: inner genes from the forward strand, and outer genes from the reverse strand, with PCGs in green, rRNAs in orange, and tRNAs in red.

Table 1 .
Mitochondrial sequences used in the phylogenetic analysis as shown in Figure3.